2.8 Gene family expansion and contraction
CAFE (version 3.1) (Hahn et al., 2007) was used to analyze gene family
expansion and contraction by comparing the S. chinensis genome
with those from eight other aphid species (namely D. vitifoliae ,S. flava, E. lanigerum, Ap. glycines, R. maidis, Ac. pisum, D.
noxia and M. persicae ). Briefly, the quantitative information of
gene families of 10 insects was obtained based on the
OrthoMCL results. The number of gene
families in each species and the trees with divergence time were used as
the input information of CAFE
(parameters set to “lambda -s, -t”). The best rates for gene birth and
death were decided using CAFE, and all branches had the same rates of
gene birth and death. Expansion and contraction of gene families were
identified using CAFE (Hahn, Demuth & Han, 2007). GO and KEGG
enrichment analyses were conducted using Omicshare CloudTools under
default instructions settings (http://www.omicshare.com/).